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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Visualizations for NGS data

This recipe will introduce some new visualizations that can be used to represent some results in NGS analysis. We will present two plots as follows:

  • A quality assessment plot for NGS
  • A map for the methylation data

Getting ready

The demonstration code presented in this recipe will use a function not available in the R package, but will obtain it from a remote host.

How to do it…

The steps for the above mentioned plots are as follows:

  1. First, start with a comprehensive plot used for visualizing the quality in a FASTQ data. You can do this within R, as you did before, by typing the following commands:
    > download.file(url = "http://biocluster.ucr.edu/~tgirke/HTML_Presentations/Manuals/Rngsapps/chipseqBioc2012/data.zip", destfile ...

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